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Refactor some tests #1

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merged 2 commits into from
Jun 27, 2019
Merged

Refactor some tests #1

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9d457f0
TST: refactor test events
Jun 26, 2019
4c9b6ea
TST: refactor test_read_raw_curry
Jun 26, 2019
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128 changes: 65 additions & 63 deletions mne/io/curry/tests/test_curry.py
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Original file line number Diff line number Diff line change
@@ -1,13 +1,15 @@
# -*- coding: UTF-8 -*-
# -*- coding: utf-8 -*-
#
# Authors: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>
#
#
# License: BSD (3-clause)

import os
import os.path as op
import numpy as np

import pytest

from numpy.testing import assert_allclose, assert_array_equal
from mne.annotations import events_from_annotations
from mne.datasets import testing
Expand All @@ -23,9 +25,9 @@
data_dir = testing.data_path(download=False)
curry_dir = op.join(data_dir, "curry")

bdf_file = op.join(data_dir, 'BDF/test_bdf_stim_channel.bdf')
bdf_file = op.join(data_dir, 'BDF', 'test_bdf_stim_channel.bdf')

bti_rfDC_file = op.join(data_dir, 'BTi/erm_HFH/c,rfDC')
bti_rfDC_file = op.join(data_dir, 'BTi', 'erm_HFH', 'c,rfDC')

curry7_rfDC_file = op.join(curry_dir, "c,rfDC Curry 7.dat")
curry8_rfDC_file = op.join(curry_dir, "c,rfDC Curry 8.cdt")
Expand All @@ -46,83 +48,83 @@
do_warn = ''


@pytest.fixture(scope='session')
def bdf_curry_ref():
"""Return a view of the reference bdf used to create the curry files."""
raw = read_raw_bdf(bdf_file, preload=True).drop_channels(['Status'])
return raw


@pytest.mark.filterwarnings(do_warn)
@testing.requires_testing_data
def test_read_raw_curry():
@pytest.mark.parametrize('fname', [
pytest.param(curry7_bdf_file, id='curry 7'),
pytest.param(curry8_bdf_file, id='curry 8'),
])
@pytest.mark.parametrize('preload', [True, False])
def test_read_raw_curry(fname, preload, bdf_curry_ref):
"""Test reading CURRY files."""
# make sure all types of files can be passed to read_raw_curry
for filename in os.listdir(curry_dir):
if "test_bdf_stim_channel Curry" in filename:
read_raw_curry(op.join(curry_dir, filename))
raw = read_raw_curry(fname, preload=preload)

if preload:
isinstance(getattr(raw, '_data'), np.ndarray)
else:
with pytest.raises(AttributeError, match="no attribute '_data'"):
getattr(raw, '_data')

assert raw.n_times == bdf_curry_ref.n_times
assert raw.info['sfreq'] == bdf_curry_ref.info['sfreq']

for field in ['kind', 'ch_name']:
assert_array_equal([ch[field] for ch in raw.info['chs']],
[ch[field] for ch in bdf_curry_ref.info['chs']])

# check no preloading for preload=False
with pytest.raises(AttributeError, match="no attribute '_data'"):
read_raw_curry(curry7_bdf_file, preload=False)._data
read_raw_curry(curry7_bdf_ascii_file, preload=False)._data
assert_allclose(raw.get_data(), bdf_curry_ref.get_data())

picks, start, stop = ["C3", "C4"], 200, 800
assert_allclose(
raw.get_data(picks=picks, start=start, stop=stop),
bdf_curry_ref.get_data(picks=picks, start=start, stop=stop),
)


@pytest.mark.filterwarnings(do_warn)
@testing.requires_testing_data
@pytest.mark.parametrize('fname,tol', [
pytest.param(curry7_rfDC_file, 1e-6, id='curry 7'),
pytest.param(curry8_rfDC_file, 1e-3, id='curry 8'), # XXX: why 1e-3?
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There are some values that turned out slightly different, maybe due to some floating point + rounding stuff? The data from these two files is read exactly the same, so i'd say this is the best we'd get of it...

])
def test_read_raw_curry_rfDC(fname, tol):
"""Test reading CURRY files."""
# check data
bti_rfDC = read_raw_bti(pdf_fname=bti_rfDC_file, head_shape_fname=None)
curry7_rfDC = read_raw_curry(curry7_rfDC_file)
curry8_rfDC = read_raw_curry(curry8_rfDC_file)
raw = read_raw_curry(fname)

# test on the eeg chans, since these were not renamed by curry
eeg_names = [ch["ch_name"] for ch in curry7_rfDC.info["chs"]
eeg_names = [ch["ch_name"] for ch in raw.info["chs"]
if ch["kind"] == FIFF.FIFFV_EEG_CH]

assert_allclose(curry7_rfDC.get_data(eeg_names),
bti_rfDC.get_data(eeg_names), rtol=1e-6)
assert_allclose(curry8_rfDC.get_data(eeg_names),
bti_rfDC.get_data(eeg_names), rtol=1e-3)

bdf = read_raw_bdf(bdf_file)
curry7_bdf = read_raw_curry(curry7_bdf_file, preload=True)
curry8_bdf = read_raw_curry(curry8_bdf_file, preload=False)
curry7_bdf_ascii = read_raw_curry(curry7_bdf_ascii_file,
preload=False)
curry8_bdf_ascii = read_raw_curry(curry7_bdf_ascii_file,
preload=True)

assert_allclose([curry7_bdf.n_times, curry7_bdf_ascii.n_times,
curry8_bdf.n_times, curry8_bdf_ascii.n_times],
bdf.n_times)
assert_allclose([curry7_bdf.info["sfreq"], curry7_bdf_ascii.info["sfreq"],
curry8_bdf.info["sfreq"], curry8_bdf_ascii.info["sfreq"]],
bdf.info["sfreq"])

# test all types of data
picks = ["C3", "C4"]
start, stop = 200, 800
for curry_file in [curry7_bdf, curry7_bdf_ascii,
curry8_bdf, curry8_bdf_ascii]:
# use chans [:3] here since curry stim chan was already extracted
assert_allclose([ch["kind"] for ch in curry_file.info["chs"]],
[ch["kind"] for ch in bdf.info["chs"][:3]])
assert_array_equal([ch["ch_name"] for ch in curry_file.info["chs"]],
[ch["ch_name"] for ch in bdf.info["chs"][:3]])
assert_allclose(curry_file.get_data(), bdf.get_data()[:3], atol=1e-6)
# can't use bdf.get_data(picks) here, since it seems bugged
assert_allclose(curry_file.get_data(picks, start, stop),
bdf.get_data(start=start, stop=stop)[:2], atol=1e-6)
assert_allclose(raw.get_data(eeg_names),
bti_rfDC.get_data(eeg_names), rtol=tol)


@testing.requires_testing_data
def test_read_events_curry():
"""Test reading curry event files."""
events = _read_events_curry(event_file, event_ids=[1, 2, 4])
bdf = read_raw_bdf(bdf_file, preload=True)
ref_events = find_events(bdf, stim_channel="Status")

assert_allclose(events, ref_events)
@pytest.mark.parametrize('fname', [
pytest.param(curry7_bdf_file, id='curry 7'),
pytest.param(curry8_bdf_file, id='curry 8'),
])
def test_read_events_curry_are_same_as_bdf(fname):
"""Test events from curry annotations recovers the right events."""
EVENT_ID = {str(ii): ii for ii in range(5)}
REF_EVENTS = find_events(read_raw_bdf(bdf_file, preload=True))

raw = read_raw_curry(curry7_bdf_file)
annot_events, _ = events_from_annotations(raw, event_id={"1": 1,
"2": 2,
"4": 4})
assert_allclose(annot_events, ref_events)
raw = read_raw_curry(fname)
events, _ = events_from_annotations(raw, event_id=EVENT_ID)
assert_allclose(events, REF_EVENTS)


def test_check_missing_files():
"""Test checking for missing curry files."""
"""Test checking for missing curry files (smoke test)."""
invalid_fname = "/invalid/path/name"

with pytest.raises(IOError, match="file type .*? must end with"):
Expand Down